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STEPdb: Sub-cellular Topologies of E.coli Polypeptides.

View: E. coli K-12 / MG1655/ ATCC 47076 proteome Export to Excel Export to HTML Export to XML Export to CSV

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E. coli K-12 / MG1655/ ATCC 47076 proteome

(mouse over and click on the one letter topology symbols to see which proteins of this specific subproteome are localized in each location)

Bacterial cell cartoon of sub-cellular locations

show distribution

Sub-cellular topologies of E.coli K-12(MG1655) proteins

2800

# Proteins
	K-12
N	405
A	2800
r	66
F1	559
B	970
F2	24
E	22
G	311
I	98
F3	9
H	68
F4	19
X	6

Manual Curation in STEP

Comments

UniProt Name:
Exopolyphosphatase (ExopolyPase) (EC 3.6.1.11) (Metaphosphatase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
25.1 ppm

show distribution

#7cb5ec

red

#7cb5ec

EcoCyc

Protein:
EG11403
Gene Locus:
ppx

Structural Annotation

SCOP

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Ribonuclease H-like motif
SCOP: 53066
HD-domain/PDEase-like
SCOP: 109603
Super Family:
Actin-like ATPase domain
SCOP: 53067
HD-domain/PDEase-like
SCOP: 109604

Protein Family Domains

Pfam domains

PFAM: P0AFL6

SMART database

SMART: ppx

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
47 % PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
29
Cleavage Score (Cmax):
0.112

LipoP 1.0

Prediction:
CYT
Cleavage site amino acid:
0
Score:
-0.200913
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
0

Phobius

Signal Peptide:
No
Number of TMs:
0

PSORTB (v3.0.2)

Localization:
Cytoplasmic
Score:
10

LocTree3

Localization:
cytoplasm
Score:
91

ClubSub-P

Localization:
Cytoplasmic

sosuiGramN

Localization:
C (cytoplasmic)

PRED-TAT

Localization:
No signal peptide predicted
Score:
0.988

TatP

Prediction:
No signal peptide predicted.

Predict Now

Manual Curation in STEP

Comments

UniProt Name:
Putative cytochrome bd-II ubiquinol oxidase subunit AppX
Localization:
Integral Inner Membrane (Probable)
Notes:
Experimentally verified orientation: N(out)-C(in).
References:
PMID: 21778229
Pseudogene/Mobile Element:
-

mRNA Expression

mRNA abundance (Taniguchi 2010)

mRNA molec/cell:
-

Protein Existence

Mass spectrometry experiments

Proteomics:
-
Proteomics / Inner Membrane fraction:
-

Protein abundance/solubility

Protein abundance (Taniguchi 2010)

Protein molec/cell:
-
PaxDb:
0 ppm

EcoCyc

Protein:
EG11114
Gene Locus:
appX

Structural Annotation

SCOP

Class:
-
Fold:
-
Super Family:
-

Protein Family Domains

Pfam domains

PFAM: P24244

SMART database

SMART: appX

Topology on the inner membrane

Orientation on the IM:
out/in (N-terminus/C-terminus)

Go to topology

Protein Complexes

Go to Complexes

Protein Hydrodynamics

Protein Solubility

Niwa et al 2009:
% PMID: 19251648

Heat-stability

Heat stable (85oC):
no PMID: 10806384

Disorder

Predict Disorder with IUPred tool:

Predict Now

Bioinformatic tools and predictions

SignalP 4.1

Signal Peptide:
No
Cleavage site amino acid:
21
Cleavage Score (Cmax):
0.107

LipoP 1.0

Prediction:
TMH
Cleavage site amino acid:
0
Score:
2.07613
Cleavage Rule:
-

TMHMM v2.0

Number of TMs:
1

Phobius

Signal Peptide:
No
Number of TMs:
1

PSORTB (v3.0.2)

Localization:
CytoplasmicMembrane
Score:
9

LocTree3

Localization:
secreted
Score:
36

ClubSub-P

Localization:
-

sosuiGramN

Localization:
unknown

PRED-TAT

Localization:
TM segment predicted: 5 - 24
Score:
0.928

TatP

Prediction:
No signal peptide predicted.

Predict Now

Protein ID (Uniprot)

Accession (Uniprot)

Gene Name (Uniprot)

Order Locus Name

Protein Name (STEPdb)

Full Name

Symbol

Uniprot

EchoLOCATION

Bernsel et al

Extracellular Appendage

First Level Targeting Chaperoning

First Level Secretion System

Second Level Targeting Chaperoning

Second Level Secretion System

K-12 Core Proteome (yes/no)

K-12 Basic Proteome (yes/no)

PPX_ECOLI

P0AFL6

ppx

b2502 JW2487

cytoplasmic peripheral IM protein, Exopolyphosphatase Ppx

Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm

A, F1

Cell membrane

Cytoplasmic

IM (predicted)

yes

APPX_ECOLI

P24244

appX

yccB

b4592 JW0961.1 b0979.1

integral IM protein (SEC in IM), Putative cytochrome bd-II ubiquinol oxidase subunit AppX

Integral Inner Membrane

Cell inner membrane

Integral Membrane Protein

N/A

SRP

SEC

yes

Records 1 to 2 of 2

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